Fig. 6

Genome-wide copy number changes in MSI tumors determined by WGS analyses. a Log2 copy number ratio plots from the WGS analysis. This analysis included all five MSI/CIN samples, as well as one MSI/CS and one MSS/CIN sample as controls. For each genomic bin (x-axis), the log2 copy number ratio calculated by CNVkit (y-axis) is plotted. The log2 ratio value of genomic segments is indicated with lines of black, red, or sky blue, representing no change, copy number gain, or loss, respectively. The dotted vertical lines separate genomic bins from different chromosomes. b Validation of chromosome arm-wide copy number events in MSI tumors using TCGA CRC samples (N = 617). Separately for MSS/MSI-L and MSI-H tumors, frequencies of copy number gain and loss are shown for each chromosome arm. Gains are shown above and losses below the labels of chromosome arms